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Ellis JR, Rowley PA. An apparent lack of synergy between degradative enzymes against Staphylococcus aureus biofilms. MicroPubl Biol 2024; 2024:10.17912/micropub.biology.001119. [PMID: 38596361 PMCID: PMC11002645 DOI: 10.17912/micropub.biology.001119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/25/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Enzymes combat bacterial infections by degrading biomolecules to disperse Staphylococcus aureus biofilms. Commercial enzyme mixtures, like cellulase and pepsin, show concentration-dependent dispersion, but low concentrations lack synergy. Only the sequential addition of pepsin followed by Arthrobacter luteus zymolyase 20T displays synergy, effectively dispersing biofilms. Purified zymolyase 100T outperforms zymolyase 20T but lacks synergy with pepsin. This study underscores the complexity of enzymatic biofilm dispersal, highlighting the need for tailored approaches based on enzyme properties and biofilm composition.
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Affiliation(s)
- Jeremy R. Ellis
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States
- The Johns Hopkins University School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States
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Elg CA, Mack E, Rolfsmeier M, McLean TC, Kosterlitz O, Soderling E, Narum S, Rowley PA, Thomas CM, Top EM. Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost. bioRxiv 2024:2024.02.05.579024. [PMID: 38370613 PMCID: PMC10871194 DOI: 10.1101/2024.02.05.579024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Plasmids play a major role in bacterial evolution and rapid adaptation by facilitating the horizontal transfer of diverse genes. Understanding how plasmids are transferred and maintained in bacterial populations is important, especially given the increasing plasmid-mediated spread of antibiotic-resistance genes to human pathogens. We investigated why broad-host range plasmid pBP136, originally isolated from clinical samples of Bordetella pertussis, quickly became extinct in laboratory Escherichia coli populations. We found that the inactivation of a previously uncharacterized plasmid gene, upf31, drastically improved long-term maintenance of the plasmid in E. coli. Loss of this single gene was associated with decreased transcription of numerous genes in the plasmid korA, korB and korC regulons, as well as changes in many chromosomal genes primarily related to metabolism. This change in transcriptome is likely initiated by Upf31 interacting with one of these major plasmid regulators, KorB. Expression of upf31 in trans not only negatively affected the persistence of a pBP136 upf31 deletion mutant, but also of the closely related archetype IncPβ plasmid R751, which is stable in E. coli and natively encodes an internally truncated upf31 allele. This suggests that whereas the upf31 allele in pBP136 might advantageously modulate gene expression in its original host, B. pertussis, the same function can have harmful effects in E. coli. Thus, using multiple hosts to study the effects of knockouts in broad-host-range plasmid genes of unknown function may reveal unexpected mechanisms that determine the fate of that plasmid in bacterial communities.
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Affiliation(s)
- Clinton A. Elg
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Erin Mack
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Michael Rolfsmeier
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Thomas C. McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Olivia Kosterlitz
- Biology Department, University of Washington, Seattle, Washington, USA
| | | | - Solana Narum
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | | | - Eva M. Top
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
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Taylor MB, Warwick AR, Skophammer R, Boyer JM, Geck RC, Gunkelman K, Walson M, Rowley PA, Dunham MJ. yEvo: A modular eukaryotic genetics and evolution research experience for high school students. Ecol Evol 2024; 14:e10811. [PMID: 38192907 PMCID: PMC10771926 DOI: 10.1002/ece3.10811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 11/26/2023] [Indexed: 01/10/2024] Open
Abstract
The resources for carrying out and analyzing microbial evolution experiments have become more accessible, making it possible to expand these studies beyond the research laboratory and into the classroom. We developed five connected, standards-aligned yeast evolution laboratory modules, called "yEvo," for high school students. The modules enable students to take agency in answering open-ended research questions. In Module 1, students evolve baker's yeast to tolerate an antifungal drug, and in subsequent modules, investigate how evolved yeasts adapted to this stressful condition at both the phenotype and genotype levels. We used pre- and post-surveys from 72 students at two different schools and post-interviews with students and teachers to assess our program goals and guide module improvement over 3 years. We measured changes in student conceptions, confidence in scientific practices, and interest in STEM careers. Students who participated in yEvo showed improvements in understanding of activity-specific concepts and reported increased confidence in designing a valid biology experiment. Student experimental data replicated literature findings and has led to new insights into antifungal resistance. The modules and provided materials, alongside "proof of concept" evaluation metrics, will serve as a model for other university researchers and K - 16 classrooms interested in engaging in open-ended research questions using yeast as a model system.
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Affiliation(s)
- M. Bryce Taylor
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
- Program in BiologyLoras CollegeDubuqueIowaUSA
| | - Alexa R. Warwick
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | | | | | - Renee C. Geck
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Kristin Gunkelman
- Department of Teacher EducationMichigan State UniversityEast LansingMichiganUSA
| | - Margaux Walson
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Paul A. Rowley
- Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
| | - Maitreya J. Dunham
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
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Ellis JR, Rowley PA. An apparent lack of synergy between degradative enzymes against Staphylococcus aureus biofilms. bioRxiv 2023:2023.10.05.561034. [PMID: 37873330 PMCID: PMC10592981 DOI: 10.1101/2023.10.05.561034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The use of enzymes represents an approach to combat bacterial infections by degrading extracellular biomolecules to disperse Staphylococcus aureus biofilms. Commercial enzyme preparations, including cellulase, amylase, pectinase, zymolyase, and pepsin, exhibit concentration-dependent dispersion of S. aureus biofilms. Here, we report that low concentrations of these enzymes generally lack synergy when combined or added together sequentially to biofilms. Only the addition of a protease (pepsin) followed by a commercial mixture of degradative enzymes from Arthrobacter luteus (zymolyase 20T), demonstrated synergy and was effective at dispersing S. aureus biofilms. A more purified mixture of Arthrobacter luteus enzymes (zymolyase 100T) showed improved dispersal of S. aureus biofilms compared to zymolyase 20T but lacked synergy with pepsin. This study emphasizes the complexity of enzymatic biofilm dispersal and the need for tailored approaches based on the properties of degradative enzymes and biofilm composition.
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Affiliation(s)
- Jeremy R Ellis
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA
- Johns Hopkins University, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Paul A Rowley
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA
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Taggart NT, Crabtree AM, Creagh JW, Bizarria R, Li S, de la Higuera I, Barnes JE, Shipley MA, Boyer JM, Stedman KM, Ytreberg FM, Rowley PA. Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae. PLoS Pathog 2023; 19:e1011418. [PMID: 37285383 PMCID: PMC10281585 DOI: 10.1371/journal.ppat.1011418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/20/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023] Open
Abstract
It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae.
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Affiliation(s)
- Nathan T Taggart
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Angela M Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jack W Creagh
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Rodolfo Bizarria
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Shunji Li
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Ignacio de la Higuera
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - Jonathan E Barnes
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
| | - Mason A Shipley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Josephine M Boyer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Kenneth M Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - F Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Department of Physics, University of Idaho, Moscow, Idaho, United States of America
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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Rowley PA, Paukner MJ, Eisenmenger LB, Field AS, Davidson RJ, Johnson SC, Asthana S, Chin NA, Prabhakaran V, Bendlin BB, Postle BR, Goldsmith HH, Carlsson CM, Brooks MA, Kalin NH, Williams LE, Rowley HA. Incidental Findings from 16,400 Brain MRI Examinations of Research Volunteers. AJNR Am J Neuroradiol 2023; 44:417-423. [PMID: 36927761 PMCID: PMC10084899 DOI: 10.3174/ajnr.a7821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND AND PURPOSE Incidental findings are discovered in neuroimaging research, ranging from trivial to life-threatening. We describe the prevalence and characteristics of incidental findings from 16,400 research brain MRIs, comparing spontaneous detection by nonradiology scanning staff versus formal neuroradiologist interpretation. MATERIALS AND METHODS We prospectively collected 16,400 brain MRIs (7782 males, 8618 females; younger than 1 to 94 years of age; median age, 38 years) under an institutional review board directive intended to identify clinically relevant incidental findings. The study population included 13,150 presumed healthy volunteers and 3250 individuals with known neurologic diagnoses. Scanning staff were asked to flag concerning imaging findings seen during the scan session, and neuroradiologists produced structured reports after reviewing every scan. RESULTS Neuroradiologists reported 13,593/16,400 (83%) scans as having normal findings, 2193/16,400 (13.3%) with abnormal findings without follow-up recommended, and 614/16,400 (3.7%) with "abnormal findings with follow-up recommended." The most common abnormalities prompting follow-up were vascular (263/614, 43%), neoplastic (130/614, 21%), and congenital (92/614, 15%). Volunteers older than 65 years of age were significantly more likely to have scans with abnormal findings (P < .001); however, among all volunteers with incidental findings, those younger than 65 years of age were more likely to be recommended for follow-up. Nonradiologists flagged <1% of MRIs containing at least 1 abnormality reported by the neuroradiologists to be concerning enough to warrant further evaluation. CONCLUSIONS Four percent of individuals who undergo research brain MRIs have an incidental, potentially clinically significant finding. Routine neuroradiologist review of all scans yields a much higher rate of significant lesion detection than selective referral from nonradiologists who perform the examinations. Workflow and scan review processes need to be carefully considered when designing research protocols.
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Affiliation(s)
- P A Rowley
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Departments of Radiology (P.A.R., LB.E., A.S.F., V.P., H.A.R.)
| | | | - L B Eisenmenger
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Departments of Radiology (P.A.R., LB.E., A.S.F., V.P., H.A.R.)
| | - A S Field
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Departments of Radiology (P.A.R., LB.E., A.S.F., V.P., H.A.R.)
| | - R J Davidson
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Psychology (R.J.D., B.R.P., H.H.G.)
| | - S C Johnson
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Wisconsin Alzheimer's Disease Research Center (S.C.J., S.A., B.B.B., C.M.C.)
- Departments of Medicine (S.C.J., S.A., N.A.C., B.B.B., C.M.C.)
| | - S Asthana
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Wisconsin Alzheimer's Disease Research Center (S.C.J., S.A., B.B.B., C.M.C.)
- Departments of Medicine (S.C.J., S.A., N.A.C., B.B.B., C.M.C.)
| | - N A Chin
- Departments of Medicine (S.C.J., S.A., N.A.C., B.B.B., C.M.C.)
| | - V Prabhakaran
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Departments of Radiology (P.A.R., LB.E., A.S.F., V.P., H.A.R.)
| | - B B Bendlin
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Wisconsin Alzheimer's Disease Research Center (S.C.J., S.A., B.B.B., C.M.C.)
- Departments of Medicine (S.C.J., S.A., N.A.C., B.B.B., C.M.C.)
| | - B R Postle
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Psychology (R.J.D., B.R.P., H.H.G.)
| | - H H Goldsmith
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Psychology (R.J.D., B.R.P., H.H.G.)
| | - C M Carlsson
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Wisconsin Alzheimer's Disease Research Center (S.C.J., S.A., B.B.B., C.M.C.)
- Departments of Medicine (S.C.J., S.A., N.A.C., B.B.B., C.M.C.)
| | - M A Brooks
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Orthopedics (M.A.B.)
| | - N H Kalin
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Psychiatry (N.H.K., L.E.W.), University of Wisconsin-Madison, Madison, Wisconsin
| | - L E Williams
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Psychiatry (N.H.K., L.E.W.), University of Wisconsin-Madison, Madison, Wisconsin
| | - H A Rowley
- From the University of Wisconsin School of Medicine and Public Health (P.A.R., L.B.E., A.S.F., R.J.D., S.C.J., S.A., V.P., B.B.B., B.R.P., H.H.G., C.M.C., M.A.B., N.H.K., L.E.W., H.A.R.)
- Departments of Radiology (P.A.R., LB.E., A.S.F., V.P., H.A.R.)
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Ellis JR, Bull JJ, Rowley PA. Fungal Glycoside Hydrolases Display Unique Specificities for Polysaccharides and Staphylococcus aureus Biofilms. Microorganisms 2023; 11:microorganisms11020293. [PMID: 36838258 PMCID: PMC9964650 DOI: 10.3390/microorganisms11020293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Commercially available cellulases and amylases can disperse the pathogenic bacteria embedded in biofilms. This suggests that polysaccharide-degrading enzymes would be useful as antibacterial therapies to aid the treatment of biofilm-associated bacteria, e.g., in chronic wounds. Using a published enzyme library, we explored the capacity of 76 diverse recombinant glycoside hydrolases to disperse Staphylococcus aureus biofilms. Four of the 76 recombinant glycoside hydrolases digested purified cellulose, amylose, or pectin. However, these enzymes did not disperse biofilms, indicating that anti-biofilm activity is not general to all glycoside hydrolases and that biofilm activity cannot be predicted from the activity on pure substrates. Only one of the 76 recombinant enzymes was detectably active in biofilm dispersion, an α-xylosidase from Aspergillus nidulans. An α-xylosidase cloned subsequently from Aspergillus thermomutatus likewise demonstrated antibiofilm activity, suggesting that α-xylosidases, in general, can disperse Staphylococcus biofilms. Surprisingly, neither of the two β-xylosidases in the library degraded biofilms. Commercial preparations of amylase and cellulase that are known to be effective in the dispersion of Staphylococcus biofilms were also analyzed. The commercial cellulase contained contaminating proteins with multiple enzymes exhibiting biofilm-dispersing activity. Successfully prospecting for additional antibiofilm enzymes may thus require large libraries and may benefit from purified enzymes. The complexity of biofilms and the diversity of glycoside hydrolases continue to make it difficult to predict or understand the enzymes that could have future therapeutic applications.
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Affiliation(s)
- Jeremy R. Ellis
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
- The Johns Hopkins University School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - James J. Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
- Correspondence:
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Crabtree AM, Taggart NT, Lee MD, Boyer JM, Rowley PA. The prevalence of killer yeasts and double-stranded RNAs in the budding yeast Saccharomyces cerevisiae. FEMS Yeast Res 2023; 23:foad046. [PMID: 37935474 PMCID: PMC10664976 DOI: 10.1093/femsyr/foad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
Killer toxins are antifungal proteins produced by many species of "killer" yeasts, including the brewer's and baker's yeast Saccharomyces cerevisiae. Screening 1270 strains of S. cerevisiae for killer toxin production found that 50% are killer yeasts, with a higher prevalence of yeasts isolated from human clinical samples and winemaking processes. Since many killer toxins are encoded by satellite double-stranded RNAs (dsRNAs) associated with mycoviruses, S. cerevisiae strains were also assayed for the presence of dsRNAs. This screen identified that 51% of strains contained dsRNAs from the mycovirus families Totiviridae and Partitiviridae, as well as satellite dsRNAs. Killer toxin production was correlated with the presence of satellite dsRNAs but not mycoviruses. However, in most killer yeasts, whole genome analysis identified the killer toxin gene KHS1 as significantly associated with killer toxin production. Most killer yeasts had unique spectrums of antifungal activities compared to canonical killer toxins, and sequence analysis identified mutations that altered their antifungal activities. The prevalence of mycoviruses and killer toxins in S. cerevisiae is important because of their known impact on yeast fitness, with implications for academic research and industrial application of this yeast species.
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Affiliation(s)
- Angela M Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, United States
| | - Nathan T Taggart
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, United States
| | - Mark D Lee
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, United States
| | - Josie M Boyer
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, United States
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, United States
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Rowley HA, Rowley PA, Field AS, Johnson SC, Carlsson CM, Asthana S, Chin NA, Bendlin BB, Okonkwo OC. Unexpected Findings from 8,205 Brain Magnetic Resonance Imaging Examinations of Research Volunteers ≥ 40 years old. Alzheimers Dement 2022. [DOI: 10.1002/alz.065845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Howard A. Rowley
- Wisconsin Alzheimer's Disease Research Center Madison WI USA
- University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - Paul A Rowley
- University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - Aaron S Field
- University of Wisconsin School of Medicine and Public Health Madison WI USA
- University of Wisconsin‐Madison Madison WI USA
| | - Sterling C. Johnson
- University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Wisconsin Alzheimer’s Institute, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Department of Medicine, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Alzheimer’s Disease Research Center, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
| | - Cynthia M. Carlsson
- Department of Medicine, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Alzheimer’s Disease Research Center, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Wisconsin Alzheimer’s Institute, University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - Sanjay Asthana
- Wisconsin Alzheimer’s Institute, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Department of Medicine, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- VA Geriatric Research, Education and Clinical Center (GRECC), William S. Middleton Memorial Veterans Hospital Madison WI USA
- Alzheimer's Disease Research Center, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
| | - Nathaniel A. Chin
- University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Wisconsin Alzheimer’s Institute, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Department of Medicine, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- VA Geriatric Research, Education and Clinical Center (GRECC), William S. Middleton Memorial Veterans Hospital Madison WI USA
| | - Barbara B. Bendlin
- University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health Madison WI USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - Ozioma C. Okonkwo
- Alzheimer's Disease Research Center, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
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10
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Taylor MB, Skophammer R, Warwick AR, Geck RC, Boyer JM, Walson M, Large CRL, Hickey ASM, Rowley PA, Dunham MJ. yEvo: Experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in S. cerevisiae. G3 Genes|Genomes|Genetics 2022; 12:6730751. [PMID: 36173330 PMCID: PMC9635649 DOI: 10.1093/g3journal/jkac246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022]
Abstract
Antifungal resistance in pathogenic fungi is a growing global health concern. Nonpathogenic laboratory strains of Saccharomyces cerevisiae are an important model for studying mechanisms of antifungal resistance that are relevant to understanding the same processes in pathogenic fungi. We have developed a series of laboratory modules in which high school students used experimental evolution to study antifungal resistance by isolating azole-resistant S. cerevisiae mutants and examining the genetic basis of resistance. We have sequenced 99 clones from these experiments and found that all possessed mutations previously shown to impact azole resistance, validating our approach. We additionally found recurrent mutations in an mRNA degradation pathway and an uncharacterized mitochondrial protein (Csf1) that have possible mechanistic connections to azole resistance. The scale of replication in this initiative allowed us to identify candidate epistatic interactions, as evidenced by pairs of mutations that occur in the same clone more frequently than expected by chance (positive epistasis) or less frequently (negative epistasis). We validated one of these pairs, a negative epistatic interaction between gain-of-function mutations in the multidrug resistance transcription factors Pdr1 and Pdr3. This high school–university collaboration can serve as a model for involving members of the broader public in the scientific process to make meaningful discoveries in biomedical research.
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Affiliation(s)
- M Bryce Taylor
- University of Washington Department of Genome Sciences, , Seattle, WA 98195 USA
- Loras College Program in Biology, , Dubuque, IA 52001 USA
| | | | - Alexa R Warwick
- Michigan State University Department of Fisheries and Wildlife, , East Lansing, MI 48824 USA
| | - Renee C Geck
- University of Washington Department of Genome Sciences, , Seattle, WA 98195 USA
| | - Josephine M Boyer
- University of Idaho Department of Biological Sciences, , Moscow, ID 83844 USA
| | - Margaux Walson
- University of Washington Department of Genome Sciences, , Seattle, WA 98195 USA
| | - Christopher R L Large
- University of Washington Department of Genome Sciences, , Seattle, WA 98195 USA
- University of Washington UW Molecular and Cellular Biology Program, , Seattle, Washington 98195 USA
| | | | - Paul A Rowley
- University of Idaho Department of Biological Sciences, , Moscow, ID 83844 USA
| | - Maitreya J Dunham
- University of Washington Department of Genome Sciences, , Seattle, WA 98195 USA
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11
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Lee MD, Creagh JW, Fredericks LR, Crabtree AM, Patel JS, Rowley PA. The Characterization of a Novel Virus Discovered in the Yeast Pichia membranifaciens. Viruses 2022; 14:v14030594. [PMID: 35337001 PMCID: PMC8951182 DOI: 10.3390/v14030594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 02/05/2023] Open
Abstract
Mycoviruses are widely distributed across fungi, including the yeasts of the Saccharomycotina subphylum. This manuscript reports the first double-stranded RNA (dsRNA) virus isolated from Pichia membranifaciens. This novel virus has been named Pichia membranifaciens virus L-A (PmV-L-A) and is a member of the Totiviridae. PmV-L-A is 4579 bp in length, with RNA secondary structures similar to the packaging, replication, and frameshift signals of totiviruses that infect Saccharomycotina yeasts. PmV-L-A was found to be part of a monophyletic group within the I-A totiviruses, implying a shared ancestry between mycoviruses isolated from the Pichiaceae and Saccharomycetaceae yeasts. Energy-minimized AlphaFold2 molecular models of the PmV-L-A Gag protein revealed structural conservation with the Gag protein of Saccharomyces cerevisiae virus L-A (ScV-L-A). The predicted tertiary structure of the PmV-L-A Pol and other homologs provided a possible mechanism for totivirus RNA replication due to structural similarities with the RNA-dependent RNA polymerases of mammalian dsRNA viruses. Insights into the structure, function, and evolution of totiviruses gained from yeasts are essential because of their emerging role in animal disease and their parallels with mammalian viruses.
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Affiliation(s)
- Mark D. Lee
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (M.D.L.); (J.W.C.); (L.R.F.); (A.M.C.); (J.S.P.)
| | - Jack W. Creagh
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (M.D.L.); (J.W.C.); (L.R.F.); (A.M.C.); (J.S.P.)
| | - Lance R. Fredericks
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (M.D.L.); (J.W.C.); (L.R.F.); (A.M.C.); (J.S.P.)
| | - Angela M. Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (M.D.L.); (J.W.C.); (L.R.F.); (A.M.C.); (J.S.P.)
| | - Jagdish Suresh Patel
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (M.D.L.); (J.W.C.); (L.R.F.); (A.M.C.); (J.S.P.)
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID 83844, USA
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (M.D.L.); (J.W.C.); (L.R.F.); (A.M.C.); (J.S.P.)
- Correspondence:
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12
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Rowley PA, Ellahi A, Han K, Patel JS, Van Leuven JT, Sawyer SL. Nuku, a family of primate retrocopies derived from KU70. G3 Genes|Genomes|Genetics 2021; 11:6283581. [PMID: 34849803 PMCID: PMC8496227 DOI: 10.1093/g3journal/jkab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/30/2021] [Indexed: 11/16/2022]
Abstract
The gene encoding the ubiquitous DNA repair protein, Ku70p, has undergone extensive copy number expansion during primate evolution. Gene duplications of KU70 have the hallmark of long interspersed element-1 mediated retrotransposition with evidence of target-site duplications, the poly-A tails, and the absence of introns. Evolutionary analysis of this expanded family of KU70-derived “NUKU” retrocopies reveals that these genes are both ancient and also actively being created in extant primate species. NUKU retrocopies show evidence of functional divergence away from KU70, as evinced by their altered pattern of tissue expression and possible tissue-specific translation. Molecular modeling predicted that amino acid changes in Nuku2p at the interaction interface with Ku80p would prevent the assembly of the Ku heterodimer. The lack of Nuku2p-Ku80p interaction was confirmed by yeast two-hybrid assay, which contrasts the robust interaction of Ku70p-Ku80p. While several NUKU retrocopies appear to have been degraded by mutation, NUKU2 shows evidence of positive natural selection, suggesting that this retrocopy is undergoing neofunctionalization. Although Nuku proteins do not appear to antagonize retrovirus transduction in cell culture, the observed expansion and rapid evolution of NUKUs could be being driven by alternative selective pressures related to infectious disease or an undefined role in primate physiology.
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Affiliation(s)
- Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Aisha Ellahi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78751, USA
| | - Kyudong Han
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Center for Bio- Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
| | - Jagdish Suresh Patel
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID 83844, USA and
| | - James T Van Leuven
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID 83844, USA and
| | - Sara L Sawyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80302, USA
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13
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Fredericks LR, Lee MD, Crabtree AM, Boyer JM, Kizer EA, Taggart NT, Roslund CR, Hunter SS, Kennedy CB, Willmore CG, Tebbe NM, Harris JS, Brocke SN, Rowley PA. The Species-Specific Acquisition and Diversification of a K1-like Family of Killer Toxins in Budding Yeasts of the Saccharomycotina. PLoS Genet 2021; 17:e1009341. [PMID: 33539346 PMCID: PMC7888664 DOI: 10.1371/journal.pgen.1009341] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/17/2021] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Killer toxins are extracellular antifungal proteins that are produced by a wide variety of fungi, including Saccharomyces yeasts. Although many Saccharomyces killer toxins have been previously identified, their evolutionary origins remain uncertain given that many of these genes have been mobilized by double-stranded RNA (dsRNA) viruses. A survey of yeasts from the Saccharomyces genus has identified a novel killer toxin with a unique spectrum of activity produced by Saccharomyces paradoxus. The expression of this killer toxin is associated with the presence of a dsRNA totivirus and a satellite dsRNA. Genetic sequencing of the satellite dsRNA confirmed that it encodes a killer toxin with homology to the canonical ionophoric K1 toxin from Saccharomyces cerevisiae and has been named K1-like (K1L). Genomic homologs of K1L were identified in six non-Saccharomyces yeast species of the Saccharomycotina subphylum, predominantly in subtelomeric regions of the genome. When ectopically expressed in S. cerevisiae from cloned cDNAs, both K1L and its homologs can inhibit the growth of competing yeast species, confirming the discovery of a family of biologically active K1-like killer toxins. The sporadic distribution of these genes supports their acquisition by horizontal gene transfer followed by diversification. The phylogenetic relationship between K1L and its genomic homologs suggests a common ancestry and gene flow via dsRNAs and DNAs across taxonomic divisions. This appears to enable the acquisition of a diverse arsenal of killer toxins by different yeast species for potential use in niche competition.
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Affiliation(s)
- Lance R. Fredericks
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Mark D. Lee
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Angela M. Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Josephine M. Boyer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Emily A. Kizer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Nathan T. Taggart
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Cooper R. Roslund
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Samuel S. Hunter
- iBEST Genomics Core, University of Idaho, Moscow, Idaho, United States of America
| | - Courtney B. Kennedy
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Cody G. Willmore
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Nova M. Tebbe
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jade S. Harris
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah N. Brocke
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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14
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Fan HF, Su BY, Ma CH, Rowley PA, Jayaram M. A bipartite thermodynamic-kinetic contribution by an activating mutation to RDF-independent excision by a phage serine integrase. Nucleic Acids Res 2020; 48:6413-6430. [PMID: 32479633 PMCID: PMC7337939 DOI: 10.1093/nar/gkaa401] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/02/2020] [Accepted: 05/08/2020] [Indexed: 12/11/2022] Open
Abstract
Streptomyces phage ϕC31 integrase (Int)—a large serine site-specific recombinase—is autonomous for phage integration (attP x attB recombination) but is dependent on the phage coded gp3, a recombination directionality factor (RDF), for prophage excision (attL x attR recombination). A previously described activating mutation, E449K, induces Int to perform attL x attR recombination in the absence of gp3, albeit with lower efficiency. E449K has no adverse effect on the competence of Int for attP x attB recombination. Int(E449K) resembles Int in gp3 mediated stimulation of attL x attR recombination and inhibition of attP x attB recombination. Using single-molecule analyses, we examined the mechanism by which E449K activates Int for gp3-independent attL x attR recombination. The contribution of E449K is both thermodynamic and kinetic. First, the mutation modulates the relative abundance of Int bound attL-attR site complexes, favoring pre-synaptic (PS) complexes over non-productively bound complexes. Roughly half of the synaptic complexes formed from Int(E449K) pre-synaptic complexes are recombination competent. By contrast, Int yields only inactive synapses. Second, E449K accelerates the dissociation of non-productively bound complexes and inactive synaptic complexes formed by Int. The extra opportunities afforded to Int(E499K) in reattempting synapse formation enhances the probability of success at fruitful synapsis.
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Affiliation(s)
- Hsiu-Fang Fan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Sizihwan, Kaohsiung 804, Taiwan.,Department of Chemistry, National Sun Yat-sen University, Sizihwan, Kaohsiung 804, Taiwan.,Aerosol Science Research Center, National Sun Yat-sen University, Sizihwan, Kaohsiung 804, Taiwan
| | - Bo-Yu Su
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chien-Hui Ma
- Department of Molecular Biosciences, UT Austin, Austin, TX 78712, USA
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, UT Austin, Austin, TX 78712, USA
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15
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Rowley PA, Samsonov AA, Betthauser TJ, Pirasteh A, Johnson SC, Eisenmenger LB. Amyloid and Tau PET Imaging of Alzheimer Disease and Other Neurodegenerative Conditions. Semin Ultrasound CT MR 2020; 41:572-583. [PMID: 33308496 DOI: 10.1053/j.sult.2020.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although diagnosing the syndrome of dementia is largely a clinical endeavor, neuroimaging plays an increasingly important role in accurately determining the underlying etiology, which extends beyond its traditional role in excluding other causes of altered cognition. New neuroimaging methods not only facilitate the diagnosis of the most common neurodegenerative conditions (particularly Alzheimer Disease [AD]) after symptom onset, but also show diagnostic promise even in the very early or presymptomatic phases of disease. Positron emission tomography (PET) is increasingly recognized as a key clinical tool for differentiating normal age-related changes in brain metabolism (using 18F-fluorodeoxyglucose [FDG]) from those seen in the earliest stages of specific forms of dementia. However, FDG PET only demonstrates nonspecific changes in altered parenchymal glucose uptake and not the specific etiologic proteinopathy causing the abnormal glucose uptake. A growing class of radiotracers targeting specific protein aggregates for amyloid-β (Aβ) and tau are changing the way AD is diagnosed, as these radiotracers directly label the underlying disease pathology. As these pathology-specific radiotracers are currently making their way to the clinic, it is important for the clinical neuroradiologist to understand the underlying patterns of Aβ and tau deposition in the context of AD (across its clinical continuum) and in other causes of dementia, as well as understand the implications of current research.
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Affiliation(s)
- Paul A Rowley
- Department of Radiology, University of Wisconsin, Madison, WI
| | | | | | - Ali Pirasteh
- Department of Radiology, University of Wisconsin, Madison, WI
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16
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Fredericks LR, Lee MD, Roslund CR, Crabtree AM, Allen PB, Rowley PA. The design and implementation of restraint devices for the injection of pathogenic microorganisms into Galleria mellonella. PLoS One 2020; 15:e0230767. [PMID: 32730254 PMCID: PMC7392296 DOI: 10.1371/journal.pone.0230767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
The injection of laboratory animals with pathogenic microorganisms poses a significant safety risk because of the potential for injury by accidental needlestick. This is especially true for researchers using invertebrate models of disease due to the required precision and accuracy of the injection. The restraint of the greater wax moth larvae (Galleria mellonella) is often achieved by grasping a larva firmly between finger and thumb. Needle resistant gloves or forceps can be used to reduce the risk of a needlestick but can result in animal injury, a loss of throughput, and inconsistencies in experimental data. Restraint devices are commonly used for the manipulation of small mammals, and in this manuscript, we describe the construction of two devices that can be used to entrap and restrain G. mellonella larvae prior to injection with pathogenic microbes. These devices reduce the manual handling of larvae and provide an engineering control to protect against accidental needlestick injury while maintaining a high rate of injection.
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Affiliation(s)
- Lance R. Fredericks
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Mark D. Lee
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Cooper R. Roslund
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Angela M. Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Peter B. Allen
- Department of Chemistry, University of Idaho, Moscow, ID, United States of America
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
- * E-mail:
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17
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Barnett BR, Casey CP, Torres-Velázquez M, Rowley PA, Yu JPJ. Convergent brain microstructure across multiple genetic models of schizophrenia and autism spectrum disorder: A feasibility study. Magn Reson Imaging 2020; 70:36-42. [PMID: 32298718 DOI: 10.1016/j.mri.2020.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/27/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2022]
Abstract
Neuroimaging studies of psychiatric illness have revealed a broad spectrum of structural and functional perturbations that have been attributed in part to the complex genetic heterogeneity underpinning these disorders. These perturbations have been identified in both preclinical genetic models and in patients when compared to control populations, but recent work has also demonstrated strong evidence for genetic, molecular, and structural convergence of several psychiatric diseases. We explored potential similarities in neural microstructure in preclinical genetic models of ASD (Fmr1, Nrxn1, Pten) and schizophrenia (Disc1 svΔ2) and in age- and sex-matched control animals with diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI). Our findings demonstrate a convergence in brain microstructure across these four genetic models with both tract-based and region-of-interest based analyses, which continues to buttress an emerging understanding of converging neural microstructure in psychiatric disease.
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Affiliation(s)
- Brian R Barnett
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Cameron P Casey
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Maribel Torres-Velázquez
- Department of Biomedical Engineering, College of Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul A Rowley
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - John-Paul J Yu
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Biomedical Engineering, College of Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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18
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Barnett BR, Anderson JM, Torres-Velázquez M, Yi SY, Rowley PA, Yu JPJ. Exercise ameliorates deficits in neural microstructure in a Disc1 model of psychiatric illness. Magn Reson Imaging 2019; 61:90-96. [PMID: 31103832 PMCID: PMC6663582 DOI: 10.1016/j.mri.2019.05.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 01/06/2023]
Abstract
Recent studies have investigated the effectiveness of aerobic exercise to improve physical and mental health outcomes in schizophrenia; however, few have explicitly explored the impact of aerobic exercise on neural microstructure, which is hypothesized to mediate the behavioral changes observed. Neural microstructure is influenced by numerous genetic factors including DISC1, which is a major molecular scaffold protein that interacts with partners like GSK3β, NDEL1, and PDE4. DISC1 has been shown to play a role in neurogenesis, neuronal migration, neuronal maturation, and synaptic signaling. As with other genetic variants that present an increased risk for disease, mutations of the DISC1 gene have been implicated in the molecular intersection of schizophrenia and numerous other major psychiatric illnesses. This study investigated whether short-term exercise recovers deficits in neural microstructure in a novel genetic Disc1 svΔ2 rat model. Disc1 svΔ2 animals and age- and sex-matched controls were subjected to a treadmill exercise protocol. Subsequent ex-vivo diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) compared neural microstructure in regions of interest (ROI) between sedentary and exercise wild-type animals and between sedentary and exercise Disc1 svΔ2 animals. Short-term exercise uncovered no significant differences in neural microstructure between sedentary and exercise control animals but did lead to significant differences between sedentary and exercise Disc1 svΔ2 animals in neocortex, basal ganglia, corpus callosum, and external capsule, suggesting a positive benefit derived from a short-term exercise regimen. Our findings suggest that Disc1 svΔ2 animals are more sensitive to the effects of short-term exercise and highlight the ameliorating potential of positive treatment interventions such as exercise on neural microstructure in genetic backgrounds of psychiatric disease susceptibility.
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Affiliation(s)
- Brian R Barnett
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jacqueline M Anderson
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Maribel Torres-Velázquez
- Department of Biomedical Engineering, College of Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sue Y Yi
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Paul A Rowley
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - John-Paul J Yu
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Biomedical Engineering, College of Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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19
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Yi SY, Barnett BR, Torres-Velázquez M, Zhang Y, Hurley SA, Rowley PA, Hernando D, Yu JPJ. Detecting Microglial Density With Quantitative Multi-Compartment Diffusion MRI. Front Neurosci 2019; 13:81. [PMID: 30837826 PMCID: PMC6389825 DOI: 10.3389/fnins.2019.00081] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/25/2019] [Indexed: 12/31/2022] Open
Abstract
Neuroinflammation plays a central role in the neuropathogenesis of a wide-spectrum of neurologic and psychiatric disease, but current neuroimaging methods to detect and characterize neuroinflammation are limited. We explored the sensitivity of quantitative multi-compartment diffusion MRI, and specifically neurite orientation dispersion and density imaging (NODDI), to detect changes in microglial density in the brain. Monte Carlo simulations of water diffusion using a NODDI acquisition scheme were performed to measure changes in a virtual MRI signal following modeled cellular changes within the extra-neurite space. 12-week-old C57BL/6J male mice (n = 48; 24 control, 24 treated with colony stimulating factor 1 receptor (CSF1R) inhibitor, PLX5622) were sacrificed at 0, 1, 3, and 7 days following withdrawal of CSF1R inhibition and were imaged ex-vivo to obtain measures of the orientation dispersion index (ODI). Following imaging, all brains were immunostained with Iba-1, NeuN, and GFAP for quantitative fluorescence microscopy. Cell populations were calculated with the ImageJ particle analyzer tool; correlation between microglial density and mean ODI values were calculated with Kendall's tau. Monte Carlo simulations demonstrate the sensitivity and positive correlation of ODI to increased occupancy in the extra-neurite space. Commensurate with our simulation data, ex-vivo NODDI imaging demonstrates an increase in ODI as microglia repopulate the brain following the withdrawal of CSF1R inhibition. Quantitative immunofluorescence of microglial density reveals that microglial density is positively correlated with ODI and greater hindered diffusion in the extra-neurite space (τ = 0.386, p < 0.05). Our results demonstrate that clinically feasible multi-compartment diffusion weighted imaging techniques such as NODDI are sensitive to microglial density and the cellular changes associated with microglial activation and highlights its potential to improve clinical diagnostic accuracy, patient risk stratification, and therapeutic monitoring of neuroinflammation in neurologic and psychiatric disease.
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Affiliation(s)
- Sue Y. Yi
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin–Madison, Madison, WI, United States
| | - Brian R. Barnett
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin–Madison, Madison, WI, United States
| | - Maribel Torres-Velázquez
- Department of Biomedical Engineering, College of Engineering, University of Wisconsin–Madison, Madison, WI, United States
| | - Yuxin Zhang
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
- Department of Medical Physics, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Samuel A. Hurley
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Paul A. Rowley
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Diego Hernando
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
- Department of Medical Physics, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - John-Paul J. Yu
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin–Madison, Madison, WI, United States
- Department of Biomedical Engineering, College of Engineering, University of Wisconsin–Madison, Madison, WI, United States
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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20
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Barnett BR, Torres-Velázquez M, Yi SY, Rowley PA, Sawin EA, Rubinstein CD, Krentz K, Anderson JM, Bakshi VP, Yu JPJ. Sex-specific deficits in neurite density and white matter integrity are associated with targeted disruption of exon 2 of the Disc1 gene in the rat. Transl Psychiatry 2019; 9:82. [PMID: 30745562 PMCID: PMC6370885 DOI: 10.1038/s41398-019-0429-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 01/24/2019] [Accepted: 01/26/2019] [Indexed: 02/06/2023] Open
Abstract
Diffusion tensor imaging (DTI) has provided remarkable insight into our understanding of white matter microstructure and brain connectivity across a broad spectrum of psychiatric disease. While DTI and other diffusion weighted magnetic resonance imaging (MRI) methods have clarified the axonal contribution to the disconnectivity seen in numerous psychiatric diseases, absent from these studies are quantitative indices of neurite density and orientation that are especially important features in regions of high synaptic density that would capture the synaptic contribution to the psychiatric disease state. Here we report the application of neurite orientation dispersion and density imaging (NODDI), an emerging microstructure imaging technique, to a novel Disc1 svΔ2 rat model of psychiatric illness and demonstrate the complementary and more specific indices of tissue microstructure found in NODDI than those reported by DTI. Our results demonstrate global and sex-specific changes in white matter microstructural integrity and deficits in neurite density as a consequence of the Disc1 svΔ2 genetic variation and highlight the application of NODDI and quantitative measures of neurite density and neurite dispersion in psychiatric disease.
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Affiliation(s)
- Brian R Barnett
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Maribel Torres-Velázquez
- Department of Biomedical Engineering, College of Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sue Y Yi
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Paul A Rowley
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Emily A Sawin
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - C Dustin Rubinstein
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kathleen Krentz
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jacqueline M Anderson
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Vaishali P Bakshi
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - John-Paul J Yu
- Neuroscience Training Program, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Biomedical Engineering, College of Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA.
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA.
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21
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Rowley PA, Guerrero-Gonzalez J, Alexander AL, Yu JPJ. Convergent microstructural brain changes across genetic models of autism spectrum disorder-A pilot study. Psychiatry Res Neuroimaging 2019; 283:83-91. [PMID: 30557783 PMCID: PMC6398946 DOI: 10.1016/j.pscychresns.2018.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 10/27/2022]
Abstract
Autism spectrum disorder (ASD) is a complex and genetically heterogeneous neuropsychiatric disease affecting as many as 1 in 68 children. Large scale genetic sequencing of individuals along the autism spectrum has uncovered several genetic risk factors for ASD; however, understanding how, and to what extent, individual genes contribute to the overall disease phenotype remains unclear. Neuroimaging studies of ASD have revealed a wide spectrum of structural and functional perturbations that are thought to reflect, in part, the complex genetic heterogeneity underpinning ASD. These perturbations, in both preclinical models and clinical patients, were identified in preclinical genetic models and ASD patients when compared to control populations; however, few studies have directly explored intrinsic differences between the models themselves. To better understand the degree and extent to which individual genes associated with ASD differ in their contribution to global measures of white matter microstructure, diffusion tensor imaging (DTI) was acquired from three novel rat genetic models of ASD (Fmr1, Nrxn1, and Pten) and DTI parameters of fractional anisotropy, mean, axial, and radial diffusivity were measured. Subsequent whole-brain voxel-wise analysis comparing each genetic model to each other (Fmr1:Nrxn1; Fmr1:Pten; Nrxn1:Pten) identified no significant differences in any comparison for all diffusion parameters assessed (FA, AD, MD, RD).
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Affiliation(s)
- Paul A Rowley
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Jose Guerrero-Gonzalez
- Department of Medical Physics, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Andrew L Alexander
- Department of Medical Physics, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Waisman Laboratory for Brain Imaging and Behavior, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Psychiatry, University of Wisconsin, School of Medicine and Public Health, Madison, WI 53705, USA
| | - John-Paul J Yu
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Psychiatry, University of Wisconsin, School of Medicine and Public Health, Madison, WI 53705, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706 USA; Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705 USA.
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22
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Crabtree AM, Kizer EA, Hunter SS, Van Leuven JT, New DD, Fagnan MW, Rowley PA. A Rapid Method for Sequencing Double-Stranded RNAs Purified from Yeasts and the Identification of a Potent K1 Killer Toxin Isolated from Saccharomyces cerevisiae. Viruses 2019; 11:v11010070. [PMID: 30654470 PMCID: PMC6356530 DOI: 10.3390/v11010070] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 12/13/2022] Open
Abstract
Mycoviruses infect a large number of diverse fungal species, but considering their prevalence, relatively few high-quality genome sequences have been determined. Many mycoviruses have linear double-stranded RNA genomes, which makes it technically challenging to ascertain their nucleotide sequence using conventional sequencing methods. Different specialist methodologies have been developed for the extraction of double-stranded RNAs from fungi and the subsequent synthesis of cDNAs for cloning and sequencing. However, these methods are often labor-intensive, time-consuming, and can require several days to produce cDNAs from double-stranded RNAs. Here, we describe a comprehensive method for the rapid extraction and sequencing of dsRNAs derived from yeasts, using short-read next generation sequencing. This method optimizes the extraction of high-quality double-stranded RNAs from yeasts and 3′ polyadenylation for the initiation of cDNA synthesis for next-generation sequencing. We have used this method to determine the sequence of two mycoviruses and a double-stranded RNA satellite present within a single strain of the model yeast Saccharomyces cerevisiae. The quality and depth of coverage was sufficient to detect fixed and polymorphic mutations within viral populations extracted from a clonal yeast population. This method was also able to identify two fixed mutations within the alpha-domain of a variant K1 killer toxin encoded on a satellite double-stranded RNA. Relative to the canonical K1 toxin, these newly reported mutations increased the cytotoxicity of the K1 toxin against a specific species of yeast.
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Affiliation(s)
- Angela M Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Emily A Kizer
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Samuel S Hunter
- IBEST Genomics Core, University of Idaho, Moscow, ID 83843, USA.
| | - James T Van Leuven
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Daniel D New
- IBEST Genomics Core, University of Idaho, Moscow, ID 83843, USA.
| | - Matthew W Fagnan
- IBEST Genomics Core, University of Idaho, Moscow, ID 83843, USA.
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
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23
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Rowley PA, Patterson K, Sandmeyer SB, Sawyer SL. Control of yeast retrotransposons mediated through nucleoporin evolution. PLoS Genet 2018; 14:e1007325. [PMID: 29694349 PMCID: PMC5918913 DOI: 10.1371/journal.pgen.1007325] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Yeasts serve as hosts to several types of genetic parasites. Few studies have addressed the evolutionary trajectory of yeast genes that control the stable co-existence of these parasites with their host cell. In Saccharomyces yeasts, the retrovirus-like Ty retrotransposons must access the nucleus. We show that several genes encoding components of the yeast nuclear pore complex have experienced natural selection for substitutions that change the encoded protein sequence. By replacing these S. cerevisiae genes with orthologs from other Saccharomyces species, we discovered that natural sequence changes have affected the mobility of Ty retrotransposons. Specifically, changing the genetic sequence of NUP84 or NUP82 to match that of other Saccharomyces species alters the mobility of S. cerevisiae Ty1 and Ty3. Importantly, all tested housekeeping functions of NUP84 and NUP82 remained equivalent across species. Signatures of natural selection, resulting in altered interactions with viruses and parasitic genetic elements, are common in host defense proteins. Yet, few instances have been documented in essential housekeeping proteins. The nuclear pore complex is the gatekeeper of the nucleus. This study shows how the evolution of this large, ubiquitous eukaryotic complex can alter the replication of a molecular parasite, but concurrently maintain essential host functionalities regarding nucleocytoplasmic trafficking.
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Affiliation(s)
- Paul A. Rowley
- BioFrontiers Institute, Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Kurt Patterson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States of America
| | - Suzanne B. Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
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24
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Rowley PA. The frenemies within: viruses, retrotransposons and plasmids that naturally infect Saccharomyces yeasts. Yeast 2017; 34:279-292. [PMID: 28387035 DOI: 10.1002/yea.3234] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/07/2022] Open
Abstract
Viruses are a major focus of current research efforts because of their detrimental impact on humanity and their ubiquity within the environment. Bacteriophages have long been used to study host-virus interactions within microbes, but it is often forgotten that the single-celled eukaryote Saccharomyces cerevisiae and related species are infected with double-stranded RNA viruses, single-stranded RNA viruses, LTR-retrotransposons and double-stranded DNA plasmids. These intracellular nucleic acid elements have some similarities to higher eukaryotic viruses, i.e. yeast retrotransposons have an analogous lifecycle to retroviruses, the particle structure of yeast totiviruses resembles the capsid of reoviruses and segregation of yeast plasmids is analogous to segregation strategies used by viral episomes. The powerful experimental tools available to study the genetics, cell biology and evolution of S. cerevisiae are well suited to further our understanding of how cellular processes are hijacked by eukaryotic viruses, retrotransposons and plasmids. This article has been written to briefly introduce viruses, retrotransposons and plasmids that infect Saccharomyces yeasts, emphasize some important cellular proteins and machineries with which they interact, and suggest the evolutionary consequences of these interactions. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Paul A Rowley
- Department of Biological Sciences, The University of Idaho, Moscow, Idaho, USA
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25
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Abstract
In eukaryotes, the degradation of cellular mRNAs is accomplished by Xrn1 and the cytoplasmic exosome. Because viral RNAs often lack canonical caps or poly-A tails, they can also be vulnerable to degradation by these host exonucleases. Yeast lack sophisticated mechanisms of innate and adaptive immunity, but do use RNA degradation as an antiviral defense mechanism. One model is that the RNA of yeast viruses is subject to degradation simply as a side effect of the intrinsic exonuclease activity of proteins involved in RNA metabolism. Contrary to this model, we find a highly refined, species-specific relationship between Xrn1p and the "L-A" totiviruses of different Saccharomyces yeast species. We show that the gene XRN1 has evolved rapidly under positive natural selection in Saccharomyces yeast, resulting in high levels of Xrn1p protein sequence divergence from one yeast species to the next. We also show that these sequence differences translate to differential interactions with the L-A virus, where Xrn1p from S. cerevisiae is most efficient at controlling the L-A virus that chronically infects S. cerevisiae, and Xrn1p from S. kudriavzevii is most efficient at controlling the L-A-like virus that we have discovered within S. kudriavzevii. All Xrn1p orthologs are equivalent in their interaction with another virus-like parasite, the Ty1 retrotransposon. Thus, the activity of Xrn1p against totiviruses is not simply an incidental consequence of the enzymatic activity of Xrn1p, but rather Xrn1p co-evolves with totiviruses to maintain its potent antiviral activity and limit viral propagation in Saccharomyces yeasts. Consistent with this, we demonstrated that Xrn1p physically interacts with the Gag protein encoded by the L-A virus, suggesting a host-virus interaction that is more complicated than just Xrn1p-mediated nucleolytic digestion of viral RNAs.
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Affiliation(s)
- Paul A. Rowley
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Brandon Ho
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Sarah Bushong
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Arlen Johnson
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
- Section of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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26
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Rowley PA, Kachroo AH, Ma CH, Maciaszek AD, Guga P, Jayaram M. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination. Nucleic Acids Res 2015; 43:6023-37. [PMID: 25999343 PMCID: PMC4499138 DOI: 10.1093/nar/gkv513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/21/2015] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
Abstract
Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.
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Affiliation(s)
- Paul A Rowley
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Aashiq H Kachroo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Anna D Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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27
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McBee RM, Rozmiarek SA, Meyerson NR, Rowley PA, Sawyer SL. The effect of species representation on the detection of positive selection in primate gene data sets. Mol Biol Evol 2015; 32:1091-6. [PMID: 25556235 PMCID: PMC4379402 DOI: 10.1093/molbev/msu399] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Over evolutionary time, both host- and virus-encoded genes have been continually selected to modify their interactions with one another. This has resulted in the rapid evolution of the specific codons that govern the physical interactions between host and virus proteins. Virologists have discovered that these evolutionary signatures, acquired in nature, can provide a shortcut in the functional dissection of host-virus interactions in the laboratory. However, the use of evolution studies in this way is complicated by the fact that many nonhuman primate species are endangered, and biomaterials are often difficult to acquire. Here, we assess how the species representation in primate gene data sets affects the detection of positive natural selection. Our results demonstrate how targeted primate sequencing projects could greatly enhance research in immunology, virology, and beyond.
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Affiliation(s)
- Ross M McBee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | | | - Nicholas R Meyerson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | - Paul A Rowley
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | - Sara L Sawyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
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28
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Meyerson NR, Rowley PA, Swan CH, Le DT, Wilkerson GK, Sawyer SL. Positive selection of primate genes that promote HIV-1 replication. Virology 2014; 454-455:291-8. [PMID: 24725956 DOI: 10.1016/j.virol.2014.02.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 02/19/2014] [Accepted: 02/28/2014] [Indexed: 12/22/2022]
Abstract
Evolutionary analyses have revealed that most host-encoded restriction factors against HIV have experienced virus-driven selection during primate evolution. However, HIV also depends on the function of many human proteins, called host factors, for its replication. It is not clear whether virus-driven selection shapes the evolution of host factor genes to the extent that it is known to shape restriction factor genes. We show that five out of 40 HIV host factor genes (13%) analyzed do bear strong signatures of positive selection. Some of these genes (CD4, NUP153, RANBP2/NUP358) have been characterized with respect to the HIV lifecycle, while others (ANKRD30A/NY-BR-1 and MAP4) remain relatively uncharacterized. One of these, ANKRD30A, shows the most rapid evolution within this set of genes and is induced by interferon stimulation. We discuss how evolutionary analysis can aid the study of host factors for viral replication, just as it has the study of host immunity systems.
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Affiliation(s)
- Nicholas R Meyerson
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Paul A Rowley
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Christina H Swan
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA; Regents School of Austin, 3230 Travis Country Circle, Austin, TX, USA
| | - Dona T Le
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Sara L Sawyer
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA.
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29
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Ma CH, Liu YT, Savva CG, Rowley PA, Cannon B, Fan HF, Russell R, Holzenburg A, Jayaram M. Organization of DNA partners and strand exchange mechanisms during Flp site-specific recombination analyzed by difference topology, single molecule FRET and single molecule TPM. J Mol Biol 2013; 426:793-815. [PMID: 24286749 DOI: 10.1016/j.jmb.2013.11.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/18/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
Abstract
Flp site-specific recombination between two target sites (FRTs) harboring non-homology within the strand exchange region does not yield stable recombinant products. In negatively supercoiled plasmids containing head-to-tail sites, the reaction produces a series of knots with odd-numbered crossings. When the sites are in head-to-head orientation, the knot products contain even-numbered crossings. Both types of knots retain parental DNA configuration. By carrying out Flp recombination after first assembling the topologically well defined Tn3 resolvase synapse, it is possible to determine whether these knots arise by a processive or a dissociative mechanism. The nearly exclusive products from head-to-head and head-to-tail oriented "non-homologous" FRT partners are a 4-noded knot and a 5-noded knot, respectively. The corresponding products from a pair of native (homologous) FRT sites are a 3-noded knot and a 4-noded catenane, respectively. These results are consistent with non-homology-induced two rounds of dissociative recombination by Flp, the first to generate reciprocal recombinants containing non-complementary base pairs and the second to produce parental molecules with restored base pairing. Single molecule fluorescence resonance energy transfer (smFRET) analysis of geometrically restricted FRTs, together with single molecule tethered particle motion (smTPM) assays of unconstrained FRTs, suggests that the sites are preferentially synapsed in an anti-parallel fashion. This selectivity in synapse geometry occurs prior to the chemical steps of recombination, signifying early commitment to a productive reaction path. The cumulative topological, smFRET and smTPM results have implications for the relative orientation of DNA partners and the directionality of strand exchange during recombination mediated by tyrosine site-specific recombinases.
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Affiliation(s)
- Chien-Hui Ma
- Section of Molecular Genetics and Microbiology, Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yen-Ting Liu
- Section of Molecular Genetics and Microbiology, Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Christos G Savva
- Microscopy and Imaging Center, Department of Biology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2257, USA
| | - Paul A Rowley
- Section of Molecular Genetics and Microbiology, Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Brian Cannon
- Department of Chemistry and Biochemistry, Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Rick Russell
- Department of Chemistry and Biochemistry, Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Andreas Holzenburg
- Microscopy and Imaging Center, Department of Biology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2257, USA
| | - Makkuni Jayaram
- Section of Molecular Genetics and Microbiology, Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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30
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Ma CH, Cui H, Hajra S, Rowley PA, Fekete C, Sarkeshik A, Ghosh SK, Yates JR, Jayaram M. Temporal sequence and cell cycle cues in the assembly of host factors at the yeast 2 micron plasmid partitioning locus. Nucleic Acids Res 2012; 41:2340-53. [PMID: 23275556 PMCID: PMC3575823 DOI: 10.1093/nar/gks1338] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Saccharomyces cerevisiae 2 micron plasmid exemplifies a benign but selfish genome, whose stability approaches that of the chromosomes of its host. The plasmid partitioning locus STB (stability locus) displays certain functional analogies with centromeres along with critical distinctions, a significant one being the absence of the kinetochore complex at STB. The remodels the structure of chromatin (RSC) chromatin remodeling complex, the nuclear motor Kip1, the histone H3 variant Cse4 and the cohesin complex associate with both loci. These factors appear to contribute to plasmid segregation either directly or indirectly through their roles in chromosome segregation. Assembly and disassembly of the plasmid-coded partitioning proteins Rep1 and Rep2 and host factors at STB follow a temporal hierarchy during the cell cycle. Assembly is initiated by STB association of [Rsc8-Rsc58], followed by [Rep1-Rep2-Kip1] and [Cse4-Rsc2-Sth1] recruitment, and culminates in cohesin assembly. Disassembly starts with dissociation of RSC components, is followed by cohesin disassembly and Cse4 exit during anaphase and late telophase, respectively. [Rep1-Rep2-Kip1] persists through G1 of the ensuing cell cycle. The de novo assembly of the 'partitioning complex' is cued by the innate cell cycle clock and is dependent on DNA replication. Shared functional attributes of STB and centromere (CEN) are consistent with a potential evolutionary link between them.
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Affiliation(s)
- Chien-Hui Ma
- Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
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Kachroo AH, Ma CH, Rowley PA, Maciaszek AD, Guga P, Jayaram M. Restoration of catalytic functions in Cre recombinase mutants by electrostatic compensation between active site and DNA substrate. Nucleic Acids Res 2010; 38:6589-601. [PMID: 20511594 PMCID: PMC2965224 DOI: 10.1093/nar/gkq466] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Two conserved catalytic arginines, Arg-173 and Arg-292, of the tyrosine site-specific recombinase Cre are essential for the transesterification steps of strand cleavage and joining in native DNA substrates containing scissile phosphate groups. The active site tyrosine (Tyr-324) provides the nucleophile for the cleavage reaction, and forms a covalent 3′-phosphotyrosyl intermediate. The 5′-hydroxyl group formed during cleavage provides the nucleophile for the joining reaction between DNA partners, yielding strand exchange. Previous work showed that substitution of the scissile phosphate (P) by methylphosphonate (MeP) permits strand cleavage by a Cre variant lacking Arg-292. We now demonstrate that MeP activation and cleavage are not blocked by substitution of Arg-173 or even simultaneous substitutions of Arg-173 and Arg-292 by alanine. Furthermore, Cre(R173A) and Cre(R292A) are competent in strand joining, Cre(R173A) being less efficient. No joining activity is detected with Cre(R173A, R292A). Consistent with their ability to cleave and join strands, Cre(R173A) and Cre(R292A) can promote recombination between two MeP-full-site DNA partners. These findings shed light on the overall contribution of active site electrostatics, and tease apart distinctive contributions of the individual arginines, to the chemical steps of recombination. They have general implications in active site mechanisms that promote important phosphoryl transfer reactions in nucleic acids.
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Affiliation(s)
- Aashiq H Kachroo
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
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Rowley PA, Kachroo AH, Ma CH, Maciaszek AD, Guga P, Jayaram M. Electrostatic suppression allows tyrosine site-specific recombination in the absence of a conserved catalytic arginine. J Biol Chem 2010; 285:22976-85. [PMID: 20448041 DOI: 10.1074/jbc.m110.112292] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The active site of the tyrosine family site-specific recombinase Flp contains a conserved catalytic pentad that includes two arginine residues, Arg-191 and Arg-308. Both arginines are essential for the transesterification steps of strand cleavage and strand joining in DNA substrates containing a phosphate group at the scissile position. During strand cleavage, the active site tyrosine supplies the nucleophile to form a covalent 3'-phosphotyrosyl intermediate. The 5'-hydroxyl group produced by cleavage provides the nucleophile to re-form a 3'-5' phosphodiester bond in a recombinant DNA strand. In previous work we showed that substitution of the scissile phosphate (P) by the charge neutral methylphosphonate (MeP) makes Arg-308 dispensable during the catalytic activation of the MeP diester bond. However, in the Flp(R308A) reaction, water out-competes the tyrosine nucleophile (Tyr-343) to cause direct hydrolysis of the MeP diester bond. We now report that for MeP activation Arg-191 is also not required. In contrast to Flp(R308A), Flp(R191A) primarily mediates normal cleavage by Tyr-343 but also exhibits a weaker direct hydrolytic activity. The cleaved MeP-tyrosyl intermediate formed by Flp(R191A) can be targeted for nucleophilic attack by a 5'-hydroxyl or water and channeled toward strand joining or hydrolysis, respectively. In collaboration with wild type Flp, Flp(R191A) promotes strand exchange between MeP- and P-DNA partners. Loss of a catalytically crucial positively charged side chain can thus be suppressed by a compensatory modification in the DNA substrate that neutralizes the negative charge on the scissile phosphate.
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Affiliation(s)
- Paul A Rowley
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA
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Abstract
The integrase (Int) from phage ϕC31 acts on the phage and host-attachment sites, attP and attB, to form an integrated prophage flanked by attL and attR. Excision (attL × attR recombination) is prevented, in the absence of accessory factors, by a putative coiled-coil motif in the C-terminal domain (CTD). Int has a serine recombinase N-terminal domain, required for synapsis of recombination substrates and catalysis. We show here that the coiled-coil motif mediates protein–protein interactions between CTDs, but only when bound to DNA. Although the histidine-tagged CTD (hCTD) was monomeric in solution, hCTD bound cooperatively to three of the recombination substrates (attB, attL and attR). Furthermore, when provided with attP and attB, hCTD brought these substrates together in a synaptic complex. Substitutions in the coiled-coil motif that greatly reduce Int integration activity, L460P and Y475H, prevented CTD–CTD interactions and led to defective DNA binding and no detectable DNA synapsis. A substitution, E449K, in full length Int confers the ability to perform excision in addition to integration as it has gained the ability to synapse attL × attR. hCTDE449K was similar to hCTD in DNA binding but unable to form the CTD synapse suggesting that the CTD synapse is not essential but could be part of the mechanism that controls directionality.
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Affiliation(s)
- Andrew R McEwan
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2BX, UK
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Rowley PA, Smith MCA, Younger E, Smith MCM. A motif in the C-terminal domain of phiC31 integrase controls the directionality of recombination. Nucleic Acids Res 2008; 36:3879-91. [PMID: 18502775 PMCID: PMC2475636 DOI: 10.1093/nar/gkn269] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Bacteriophage ϕC31 encodes an integrase, which acts on the phage and host attachment sites, attP and attB, to form an integrated prophage flanked by attL and attR. In the absence of accessory factors, ϕC31 integrase cannot catalyse attL x attR recombination to excise the prophage. To understand the mechanism of directionality, mutant integrases were characterized that were active in excision. A hyperactive integrase, Int E449K, gained the ability to catalyse attL x attR, attL x attL and attR x attR recombination whilst retaining the ability to recombine attP x attB. A catalytically defective derivative of this mutant, Int S12A, E449K, could form stable complexes with attP/attB, attL/attR, attL/attL and attR/attR under conditions where Int S12A only complexed with attP/attB. Further analysis of the Int E449K-attL/attR synaptic events revealed a preference for one of the two predicted synapse structures with different orientations of the attL/attR sites. Several amino acid substitutions conferring hyperactivity, including E449K, were localized to one face of a predicted coiled-coil motif in the C-terminal domain. This work shows that a motif in the C-terminal domain of ϕC31 integrase controls the formation of the synaptic interface in both integration and excision, possibly through a direct role in protein–protein interactions.
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Affiliation(s)
- Paul A Rowley
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB252ZD, UK
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